1civ: Difference between revisions
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< | ==CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS== | ||
The | <StructureSection load='1civ' size='340' side='right'caption='[[1civ]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1civ]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flaveria_bidentis Flaveria bidentis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CIV FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1civ FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1civ OCA], [https://pdbe.org/1civ PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1civ RCSB], [https://www.ebi.ac.uk/pdbsum/1civ PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1civ ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MDHP_FLABI MDHP_FLABI] The chloroplastic, NADP-dependent form is essential for the photosynthesis C4 cycle, which allows plants to circumvent the problem of photorespiration. In C4 plants, NADP-MDH activity acts to convert oxaloacetate to malate in chloroplasts of mesophyll cells for transport to the bundle sheath cells. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/1civ_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1civ ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: NADP-dependent malate dehydrogenase (EC 1.1.1.82) is a light-activated chloroplast enzyme that functions in the C4 pathway of photosynthesis. The light regulation is believed to be mediated in vivo by thioredoxin-catalyzed reduction and re-oxidation of cystine residues. The rates of reversible activation and inactivation of the enzyme are strongly influenced by the coenzyme substrates that seem to ultimately determine the steady-state extent of activation in vivo. RESULTS: The X-ray structure of the inactive, oxidized enzyme was determined at 2.8 A resolution. The core structure is homologous to AND-dependent malate dehydrogenases. Two surface-exposed and thioredoxin-accessible disulfide bonds are present, one in the N-terminal extension and the other in the C-terminal extension. The C-terminal peptide of the inactive, oxidized enzyme is constrained by its disulfide bond to fold into the active site over NADP+, hydrogen bonding to the catalytic His225 as well as obstructing access of the C4 acid substrate. Two loops flanking the active site, termed the Arg2 and Trp loops, that contain the C4 acid substrate binding residues are prevented from closing by the C-terminal extension. CONCLUSIONS: The structure explains the role of the C-terminal extension in inhibiting activity. The negative C terminus will interact more strongly with the positively charged nicotinamide of NADP+ than NADPH, explaining why the coenzyme-binding affinities of the enzyme differ so markedly from those of all other homologous alpha-hydroxy acid dehydrogenases. NADP+ may also slow dissociation of the C terminus upon reduction, providing a mechanism for the inhibition of activation by NADP+ but not NADPH. | |||
Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction.,Carr PD, Verger D, Ashton AR, Ollis DL Structure. 1999 Apr 15;7(4):461-75. PMID:10196131<ref>PMID:10196131</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1civ" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
[[Category: Flaveria bidentis]] | [[Category: Flaveria bidentis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Ashton | [[Category: Ashton AR]] | ||
[[Category: Carr | [[Category: Carr PD]] | ||
[[Category: Ollis | [[Category: Ollis DL]] | ||
[[Category: Verger | [[Category: Verger D]] | ||
Latest revision as of 08:52, 9 August 2023
CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTISCHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS
Structural highlights
FunctionMDHP_FLABI The chloroplastic, NADP-dependent form is essential for the photosynthesis C4 cycle, which allows plants to circumvent the problem of photorespiration. In C4 plants, NADP-MDH activity acts to convert oxaloacetate to malate in chloroplasts of mesophyll cells for transport to the bundle sheath cells. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedBACKGROUND: NADP-dependent malate dehydrogenase (EC 1.1.1.82) is a light-activated chloroplast enzyme that functions in the C4 pathway of photosynthesis. The light regulation is believed to be mediated in vivo by thioredoxin-catalyzed reduction and re-oxidation of cystine residues. The rates of reversible activation and inactivation of the enzyme are strongly influenced by the coenzyme substrates that seem to ultimately determine the steady-state extent of activation in vivo. RESULTS: The X-ray structure of the inactive, oxidized enzyme was determined at 2.8 A resolution. The core structure is homologous to AND-dependent malate dehydrogenases. Two surface-exposed and thioredoxin-accessible disulfide bonds are present, one in the N-terminal extension and the other in the C-terminal extension. The C-terminal peptide of the inactive, oxidized enzyme is constrained by its disulfide bond to fold into the active site over NADP+, hydrogen bonding to the catalytic His225 as well as obstructing access of the C4 acid substrate. Two loops flanking the active site, termed the Arg2 and Trp loops, that contain the C4 acid substrate binding residues are prevented from closing by the C-terminal extension. CONCLUSIONS: The structure explains the role of the C-terminal extension in inhibiting activity. The negative C terminus will interact more strongly with the positively charged nicotinamide of NADP+ than NADPH, explaining why the coenzyme-binding affinities of the enzyme differ so markedly from those of all other homologous alpha-hydroxy acid dehydrogenases. NADP+ may also slow dissociation of the C terminus upon reduction, providing a mechanism for the inhibition of activation by NADP+ but not NADPH. Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction.,Carr PD, Verger D, Ashton AR, Ollis DL Structure. 1999 Apr 15;7(4):461-75. PMID:10196131[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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